Chromatin “pre-pattern” and epigenetic modulation in the cell fate choice of liver over pancreas in the endoderm

References

• Meissner A. Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 2010; 28:1079 - 88; http://dx.doi.org/10.1038/nbt.1684; PMID: 20944600
   PubMed Web of Science ®Google Scholar
• Young RA. Control of the embryonic stem cell state. Cell 2011; 144:940 - 54; http://dx.doi.org/10.1016/j.cell.2011.01.032; PMID: 21414485
   PubMed Web of Science ®Google Scholar
• Fisher CL, Fisher AG. Chromatin states in pluripotent, differentiated, and reprogrammed cells. Curr Opin Genet Dev 2011; 21:140 - 6; http://dx.doi.org/10.1016/j.gde.2011.01.015; PMID: 21316216
   PubMed Web of Science ®Google Scholar
• Hemberger M, Dean W, Reik W. Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington’s canal. Nat Rev Mol Cell Biol 2009; 10:526 - 37; http://dx.doi.org/10.1038/nrm2727; PMID: 19603040
   PubMed Web of Science ®Google Scholar
• Chambers D, Mason I. Expression of sprouty2 during early development of the chick embryo is coincident with known sites of FGF signalling. Mech Dev 2000; 91:361 - 4; http://dx.doi.org/10.1016/S0925-4773(99)00288-9; PMID: 10704865
   PubMed Web of Science ®Google Scholar
• Niwa H, Miyazaki J, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 2000; 24:372 - 6; http://dx.doi.org/10.1038/74199; PMID: 10742100
   PubMed Web of Science ®Google Scholar
• Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005; 122:947 - 56; http://dx.doi.org/10.1016/j.cell.2005.08.020; PMID: 16153702
   PubMed Web of Science ®Google Scholar
• Kim J, Chu J, Shen X, Wang J, Orkin SH. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008; 132:1049 - 61; http://dx.doi.org/10.1016/j.cell.2008.02.039; PMID: 18358816
   PubMed Web of Science ®Google Scholar
• Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006; 125:315 - 26; http://dx.doi.org/10.1016/j.cell.2006.02.041; PMID: 16630819
   PubMed Web of Science ®Google Scholar
• Meshorer E, Yellajoshula D, George E, Scambler PJ, Brown DT, Misteli T. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 2006; 10:105 - 16; http://dx.doi.org/10.1016/j.devcel.2005.10.017; PMID: 16399082
   PubMed Web of Science ®Google Scholar
• Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011; 470:279 - 83; http://dx.doi.org/10.1038/nature09692; PMID: 21160473
   PubMed Web of Science ®Google Scholar
• Zaret KS. Regulatory phases of early liver development: paradigms of organogenesis. Nat Rev Genet 2002; 3:499 - 512; http://dx.doi.org/10.1038/nrg837; PMID: 12094228
   PubMed Web of Science ®Google Scholar
• Zaret KS. Genetic programming of liver and pancreas progenitors: lessons for stem-cell differentiation. Nat Rev Genet 2008; 9:329 - 40; http://dx.doi.org/10.1038/nrg2318; PMID: 18398419
   PubMed Web of Science ®Google Scholar
• Deutsch G, Jung J, Zheng M, Lóra J, Zaret KS. A bipotential precursor population for pancreas and liver within the embryonic endoderm. Development 2001; 128:871 - 81; PMID: 11222142
   PubMed Web of Science ®Google Scholar
• Bort R, Martinez-Barbera JP, Beddington RS, Zaret KS. Hex homeobox gene-dependent tissue positioning is required for organogenesis of the ventral pancreas. Development 2004; 131:797 - 806; http://dx.doi.org/10.1242/dev.00965; PMID: 14736744
   PubMed Web of Science ®Google Scholar
• Chung WS, Shin CH, Stainier DY. Bmp2 signaling regulates the hepatic versus pancreatic fate decision. Dev Cell 2008; 15:738 - 48; http://dx.doi.org/10.1016/j.devcel.2008.08.019; PMID: 19000838
   PubMed Web of Science ®Google Scholar
• Gualdi R, Bossard P, Zheng M, Hamada Y, Coleman JR, Zaret KS. Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control. Genes Dev 1996; 10:1670 - 82; http://dx.doi.org/10.1101/gad.10.13.1670; PMID: 8682297
   PubMed Web of Science ®Google Scholar
• Bossard P, Zaret KS. GATA transcription factors as potentiators of gut endoderm differentiation. Development 1998; 125:4909 - 17; PMID: 9811575
   PubMed Web of Science ®Google Scholar
• Cirillo LA, Lin FR, Cuesta I, Friedman D, Jarnik M, Zaret KS. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol Cell 2002; 9:279 - 89; http://dx.doi.org/10.1016/S1097-2765(02)00459-8; PMID: 11864602
   PubMed Web of Science ®Google Scholar
• Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 2005; 122:33 - 43; http://dx.doi.org/10.1016/j.cell.2005.05.008; PMID: 16009131
   PubMed Web of Science ®Google Scholar
• Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 2008; 132:958 - 70; http://dx.doi.org/10.1016/j.cell.2008.01.018; PMID: 18358809
   PubMed Web of Science ®Google Scholar
• Lee CS, Friedman JR, Fulmer JT, Kaestner KH. The initiation of liver development is dependent on Foxa transcription factors. Nature 2005; 435:944 - 7; http://dx.doi.org/10.1038/nature03649; PMID: 15959514
   PubMed Web of Science ®Google Scholar
• Holtzinger A, Evans T. Gata4 regulates the formation of multiple organs. Development 2005; 132:4005 - 14; http://dx.doi.org/10.1242/dev.01978; PMID: 16079152
   PubMed Web of Science ®Google Scholar
• Zhao R, Watt AJ, Li J, Luebke-Wheeler J, Morrisey EE, Duncan SA. GATA6 is essential for embryonic development of the liver but dispensable for early heart formation. Mol Cell Biol 2005; 25:2622 - 31; http://dx.doi.org/10.1128/MCB.25.7.2622-2631.2005; PMID: 15767668
   PubMed Web of Science ®Google Scholar
• Watt AJ, Zhao R, Li J, Duncan SA. Development of the mammalian liver and ventral pancreas is dependent on GATA4. BMC Dev Biol 2007; 7:37; http://dx.doi.org/10.1186/1471-213X-7-37; PMID: 17451603
   PubMed Web of Science ®Google Scholar
• Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev 2011; 25:2227 - 41; http://dx.doi.org/10.1101/gad.176826.111; PMID: 22056668
   PubMed Web of Science ®Google Scholar
• Sekiya T, Zaret KS. Repression by Groucho/TLE/Grg proteins: genomic site recruitment generates compacted chromatin in vitro and impairs activator binding in vivo. Mol Cell 2007; 28:291 - 303; http://dx.doi.org/10.1016/j.molcel.2007.10.002; PMID: 17964267
   PubMed Web of Science ®Google Scholar
• Santisteban P, Recacha P, Metzger DE, Zaret KS. Dynamic expression of Groucho-related genes Grg1 and Grg3 in foregut endoderm and antagonism of differentiation. Dev Dyn 2010; 239:980 - 6; http://dx.doi.org/10.1002/dvdy.22217; PMID: 20108349
   PubMed Web of Science ®Google Scholar
• Jonsson J, Carlsson L, Edlund T, Edlund H. Insulin-promoter-factor 1 is required for pancreas development in mice. Nature 1994; 371:606 - 9; http://dx.doi.org/10.1038/371606a0; PMID: 7935793
   PubMed Web of Science ®Google Scholar
• Guz Y, Montminy MR, Stein R, Leonard J, Gamer LW, Wright CV, et al. Expression of murine STF-1, a putative insulin gene transcription factor, in beta cells of pancreas, duodenal epithelium and pancreatic exocrine and endocrine progenitors during ontogeny. Development 1995; 121:11 - 8; PMID: 7867492
   PubMed Web of Science ®Google Scholar
• Offield MF, Jetton TL, Labosky PA, Ray M, Stein RW, Magnuson MA, et al. PDX-1 is required for pancreatic outgrowth and differentiation of the rostral duodenum. Development 1996; 122:983 - 95; PMID: 8631275
   PubMed Web of Science ®Google Scholar
• Jung J, Zheng M, Goldfarb M, Zaret KS. Initiation of mammalian liver development from endoderm by fibroblast growth factors. Science 1999; 284:1998 - 2003; http://dx.doi.org/10.1126/science.284.5422.1998; PMID: 10373120
   PubMed Web of Science ®Google Scholar
• Rossi JM, Dunn NR, Hogan BL, Zaret KS. Distinct mesodermal signals, including BMPs from the septum transversum mesenchyme, are required in combination for hepatogenesis from the endoderm. Genes Dev 2001; 15:1998 - 2009; http://dx.doi.org/10.1101/gad.904601; PMID: 11485993
   PubMed Web of Science ®Google Scholar
• Calmont A, Wandzioch E, Tremblay KD, Minowada G, Kaestner KH, Martin GR, et al. An FGF response pathway that mediates hepatic gene induction in embryonic endoderm cells. Dev Cell 2006; 11:339 - 48; http://dx.doi.org/10.1016/j.devcel.2006.06.015; PMID: 16950125
   PubMed Web of Science ®Google Scholar
• Wandzioch E, Zaret KS. Dynamic signaling network for the specification of embryonic pancreas and liver progenitors. Science 2009; 324:1707 - 10; http://dx.doi.org/10.1126/science.1174497; PMID: 19556507
   PubMed Web of Science ®Google Scholar
• Sosa-Pineda B, Wigle JT, Oliver G. Hepatocyte migration during liver development requires Prox1. Nat Genet 2000; 25:254 - 5; http://dx.doi.org/10.1038/76996; PMID: 10888866
   PubMed Web of Science ®Google Scholar
• Burke Z, Oliver G. Prox1 is an early specific marker for the developing liver and pancreas in the mammalian foregut endoderm. Mech Dev 2002; 118:147 - 55; http://dx.doi.org/10.1016/S0925-4773(02)00240-X; PMID: 12351178
   PubMed Web of Science ®Google Scholar
• Jacquemin P, Lemaigre FP, Rousseau GG. The Onecut transcription factor HNF-6 (OC-1) is required for timely specification of the pancreas and acts upstream of Pdx-1 in the specification cascade. Dev Biol 2003; 258:105 - 16; http://dx.doi.org/10.1016/S0012-1606(03)00115-5; PMID: 12781686
   PubMed Web of Science ®Google Scholar
• Haumaitre C, Barbacci E, Jenny M, Ott MO, Gradwohl G, Cereghini S. Lack of TCF2/vHNF1 in mice leads to pancreas agenesis. Proc Natl Acad Sci U S A 2005; 102:1490 - 5; http://dx.doi.org/10.1073/pnas.0405776102; PMID: 15668393
   PubMed Web of Science ®Google Scholar
• Lokmane L, Haumaitre C, Garcia-Villalba P, Anselme I, Schneider-Maunoury S, Cereghini S. Crucial role of vHNF1 in vertebrate hepatic specification. Development 2008; 135:2777 - 86; http://dx.doi.org/10.1242/dev.023010; PMID: 18635606
   PubMed Web of Science ®Google Scholar
• Xu CR, Cole PA, Meyers DJ, Kormish J, Dent S, Zaret KS. Chromatin “prepattern” and histone modifiers in a fate choice for liver and pancreas. Science 2011; 332:963 - 6; http://dx.doi.org/10.1126/science.1202845; PMID: 21596989
   PubMed Web of Science ®Google Scholar
• Azuara V, Perry P, Sauer S, Spivakov M, Jørgensen HF, John RM, et al. Chromatin signatures of pluripotent cell lines. Nat Cell Biol 2006; 8:532 - 8; http://dx.doi.org/10.1038/ncb1403; PMID: 16570078
   PubMed Web of Science ®Google Scholar
• Yao TP, Oh SP, Fuchs M, Zhou ND, Ch’ng LE, Newsome D, et al. Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell 1998; 93:361 - 72; http://dx.doi.org/10.1016/S0092-8674(00)81165-4; PMID: 9590171
   PubMed Web of Science ®Google Scholar
• Xu W, Edmondson DG, Evrard YA, Wakamiya M, Behringer RR, Roth SY. Loss of Gcn5l2 leads to increased apoptosis and mesodermal defects during mouse development. Nat Genet 2000; 26:229 - 32; http://dx.doi.org/10.1038/79973; PMID: 11017084
   PubMed Web of Science ®Google Scholar
• Yamauchi T, Yamauchi J, Kuwata T, Tamura T, Yamashita T, Bae N, et al. Distinct but overlapping roles of histone acetylase PCAF and of the closely related PCAF-B/GCN5 in mouse embryogenesis. Proc Natl Acad Sci U S A 2000; 97:11303 - 6; http://dx.doi.org/10.1073/pnas.97.21.11303; PMID: 11027331
   PubMed Web of Science ®Google Scholar
• Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 2005; 6:838 - 49; http://dx.doi.org/10.1038/nrm1761; PMID: 16261189
   PubMed Web of Science ®Google Scholar
• Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002; 298:1039 - 43; http://dx.doi.org/10.1126/science.1076997; PMID: 12351676
   PubMed Web of Science ®Google Scholar
• van Arensbergen J, García-Hurtado J, Moran I, Maestro MA, Xu X, Van de Casteele M, et al. Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program. Genome Res 2010; 20:722 - 32; http://dx.doi.org/10.1101/gr.101709.109; PMID: 20395405
   PubMed Web of Science ®Google Scholar
• Derynck R, Zhang YE. Smad-dependent and Smad-independent pathways in TGF-beta family signalling. Nature 2003; 425:577 - 84; http://dx.doi.org/10.1038/nature02006; PMID: 14534577
   PubMed Web of Science ®Google Scholar
• Pouponnot C, Jayaraman L, Massagué J. Physical and functional interaction of SMADs and p300/CBP. J Biol Chem 1998; 273:22865 - 8; http://dx.doi.org/10.1074/jbc.273.36.22865; PMID: 9722503
   PubMed Web of Science ®Google Scholar
• de Caestecker MP, Yahata T, Wang D, Parks WT, Huang S, Hill CS, et al. The Smad4 activation domain (SAD) is a proline-rich, p300-dependent transcriptional activation domain. J Biol Chem 2000; 275:2115 - 22; http://dx.doi.org/10.1074/jbc.275.3.2115; PMID: 10636916
   PubMed Web of Science ®Google Scholar
• Chu GC, Dunn NR, Anderson DC, Oxburgh L, Robertson EJ. Differential requirements for Smad4 in TGFbeta-dependent patterning of the early mouse embryo. Development 2004; 131:3501 - 12; http://dx.doi.org/10.1242/dev.01248; PMID: 15215210
   PubMed Web of Science ®Google Scholar
• Xu J, Pope SD, Jazirehi AR, Attema JL, Papathanasiou P, Watts JA, et al. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci U S A 2007; 104:12377 - 82; http://dx.doi.org/10.1073/pnas.0704579104; PMID: 17640912
   PubMed Web of Science ®Google Scholar
• Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, et al. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev 2009; 23:2824 - 38; http://dx.doi.org/10.1101/gad.1861209; PMID: 20008934
   PubMed Web of Science ®Google Scholar
• Taube JH, Allton K, Duncan SA, Shen L, Barton MC. Foxa1 functions as a pioneer transcription factor at transposable elements to activate Afp during differentiation of embryonic stem cells. J Biol Chem 2010; 285:16135 - 44; http://dx.doi.org/10.1074/jbc.M109.088096; PMID: 20348100
   PubMed Web of Science ®Google Scholar
• Minaee S, Farmer D, Georgiou A, Sabbattini P, Webster Z, Chow CM, et al. Mapping and functional analysis of regulatory sequences in the mouse lambda5-VpreB1 domain. Mol Immunol 2005; 42:1283 - 92; http://dx.doi.org/10.1016/j.molimm.2005.01.003; PMID: 15950724
   PubMed Web of Science ®Google Scholar
• Liber D, Domaschenz R, Holmqvist PH, Mazzarella L, Georgiou A, Leleu M, et al. Epigenetic priming of a pre-B cell-specific enhancer through binding of Sox2 and Foxd3 at the ESC stage. Cell Stem Cell 2010; 7:114 - 26; http://dx.doi.org/10.1016/j.stem.2010.05.020; PMID: 20621055
   PubMed Web of Science ®Google Scholar
• Lis JT. Imaging Drosophila gene activation and polymerase pausing in vivo. Nature 2007; 450:198 - 202; http://dx.doi.org/10.1038/nature06324; PMID: 17994086
   PubMed Web of Science ®Google Scholar
• Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci U S A 2008; 105:7762 - 7; http://dx.doi.org/10.1073/pnas.0802406105; PMID: 18505835
   PubMed Web of Science ®Google Scholar
• Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 2010; 327:335 - 8; http://dx.doi.org/10.1126/science.1181421; PMID: 20007866
   PubMed Web of Science ®Google Scholar
• Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, et al. c-Myc regulates transcriptional pause release. Cell 2010; 141:432 - 45; http://dx.doi.org/10.1016/j.cell.2010.03.030; PMID: 20434984
   PubMed Web of Science ®Google Scholar